5QBW

Crystal structure of human Cathepsin-S with bound ligand

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.148 

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This is version 2.2 of the entry. See complete history. 


Literature

Crystal structure of human Cathepsin-S with bound ligand

Bembenek, S.D., Ameriks, M.K., Mirzadegan, T., Yang, H., Shao, C., Burley, S.K.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin S223Homo sapiensMutation(s): 1 
Gene Names: CTSS
EC: 3.4.22.27
UniProt & NIH Common Fund Data Resources
Find proteins for P25774 (Homo sapiens)
Explore P25774 
Go to UniProtKB:  P25774
PHAROS:  P25774
GTEx:  ENSG00000163131 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25774
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B8S
Query on B8S
Download Ideal Coordinates CCD File 
B [auth A]N-{[2-chloro-5-(2-{3-[4-(6-chloro-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propyl}-3-oxo-2,3-dihydropyridazin-4-yl)phenyl]methyl}-4-fluorobenzamide
C34 H33 Cl2 F N6 O3
LWFRBSJHBRLMJP-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
B8S BindingDB:  5QBW IC50: min: 60, max: 1800 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.148 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.015α = 90
b = 71.015β = 90
c = 88.714γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Structure summary
  • Version 2.0: 2018-06-06
    Changes: Atomic model, Data collection, Other, Refinement description
  • Version 2.1: 2021-02-10
    Changes: Database references, Structure summary
  • Version 2.2: 2021-11-17
    Changes: Database references, Structure summary